Peter Kollman
#26,101
Most Influential Person Now
American chemist
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Chemistry
Peter Kollman's Degrees
- PhD Chemistry University of California, Berkeley
- Bachelors Chemistry University of California, Berkeley
Why Is Peter Kollman Influential?
(Suggest an Edit or Addition)According to Wikipedia, Peter Andrew Kollman was a professor of chemistry and pharmaceutical chemistry at the University of California, San Francisco. He is known for his work in computational chemistry, molecular modeling and bioinformatics, especially for his role in the development of the AMBER force field and molecular dynamics software package.
Peter Kollman's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Development and testing of a general amber force field (2004) (12497)
- A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules (1995) (10909)
- Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models (1992) (5527)
- A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char (1993) (5449)
- THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method (1992) (5125)
- A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS (1984) (4134)
- A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations (2003) (3886)
- Automatic atom type and bond type perception in molecular mechanical calculations. (2006) (3834)
- Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. (2000) (3726)
- How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? (2000) (3290)
- An all atom force field for simulations of proteins and nucleic acids (1986) (2837)
- An approach to computing electrostatic charges for molecules (1984) (2577)
- AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules (1995) (2567)
- Atomic charges derived from semiempirical methods (1990) (2488)
- FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA (1993) (1695)
- Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices (1998) (1338)
- Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. (1998) (1223)
- AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions (1981) (1068)
- Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation (1993) (1029)
- A second generation force field for the simulation of proteins (1996) (1008)
- A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers (1986) (829)
- Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins (1995) (819)
- A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. (1999) (799)
- Encyclopedia of computational chemistry (1998) (738)
- The maximal affinity of ligands. (1999) (721)
- Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding (2000) (706)
- Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies (1999) (692)
- Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins (1995) (684)
- Multidimensional free‐energy calculations using the weighted histogram analysis method (1995) (652)
- Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. (2001) (637)
- Theory of the hydrogen bond (1972) (581)
- Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. (2001) (490)
- Electrostatic recognition between superoxide and copper, zinc superoxide dismutase (1983) (472)
- Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. (2000) (452)
- Application of the RESP Methodology in the Parametrization of Organic Solvents (1998) (410)
- Free energy calculations by computer simulation. (1987) (369)
- Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and N-Methylacetamide (1995) (345)
- Theoretical studies of hydrogen-bonded dimers. Complexes involving HF, H2O, NH3, CH1, H2S, PH3, HCN, HNC, HCP, CH2NH, H2CS, H2CO, CH4, CF3,H, C2H2, C2H4, C6H6, F- and H3O+ (1975) (326)
- Ion solvation in polarizable water: molecular dynamics simulations (1991) (292)
- Electrostatic potential molecular surfaces. (1982) (288)
- Molecular dynamics simulation of nucleic acids. (2000) (287)
- Computational alanine scanning of the 1:1 human growth hormone–receptor complex (2002) (281)
- Implementation of nonadditive intermolecular potentials by use of molecular dynamics: development of a water-water potential and water-ion cluster interactions (1990) (275)
- Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. (2000) (269)
- Calculation of the relative change in binding free energy of a protein-inhibitor complex. (1987) (264)
- A general analysis of noncovalent intermolecular interactions (1977) (240)
- Lactonization is the critical first step in the disposition of the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor atorvastatin. (2000) (232)
- Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance (2001) (230)
- Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules (1996) (229)
- Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. (1999) (228)
- Benzene Dimer: A Good Model for π−π Interactions in Proteins? A Comparison between the Benzene and the Toluene Dimers in the Gas Phase and in an Aqueous Solution (1996) (224)
- A molecular-mechanics study of 18-crown-6 and its alkali complexes: an analysis of structural flexibility, ligand specificity, and the macrocyclic effect (1982) (220)
- Computational study of the structural, energetic, and acid-base properties of calix[4]arenes (1990) (219)
- On low-barrier hydrogen bonds and enzyme catalysis. (1995) (217)
- Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. (1996) (217)
- Cation-.pi. Interactions: Nonadditive Effects Are Critical in Their Accurate Representation (1995) (217)
- The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data (1997) (213)
- Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models (2001) (208)
- Molecular dynamics simulations highlight the structural differences among DNA: DNA, RNA:RNA, and DNA:RNA hybrid duplexes (1997) (197)
- Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. (2003) (190)
- Continuum solvent studies of the stability of RNA hairpin loops and helices. (1998) (189)
- Water–water and water–ion potential functions including terms for many body effects (1985) (185)
- Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin (1987) (183)
- Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches (1993) (182)
- Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field"Journal of Computational Chemistry(2004) 25(9) 1157–1174 (2005) (174)
- Use of MM‐PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece (2000) (174)
- Theory of the Hydrogen Bond: Electronic Structure and Properties of the Water Dimer (1969) (171)
- New-generation amber united-atom force field. (2006) (167)
- Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. (1998) (163)
- Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. (2002) (159)
- An application of the functional Boys-Bernardi counterpoise method to molecular potential surfaces (1973) (158)
- The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. (1998) (151)
- Methoxy group nonplanarity in o-dimethoxybenzenes. Simple predictive models for conformations and rotational barriers in alkoxyaromatics (1979) (151)
- Theoretical Investigation of the Hydrogen Bond Strengths in Guanine-Cytosine and Adenine-Thymine Base Pairs (1994) (146)
- Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation (2002) (146)
- Flexible ligand docking: A multistep strategy approach (1999) (145)
- Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. (2000) (144)
- Molecular dynamics in the endgame of protein structure prediction. (2001) (143)
- An analysis of current methodologies for conformational searching of complex molecules. (1988) (137)
- On loop folding in nucleic acid hairpin-type structures. (1986) (131)
- What determines the van der Waals coefficient β in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? (1999) (130)
- Hydrogen bonding ability of the amide group (1974) (130)
- Investigation of Structure, Dynamics, and Solvation in 1-Octanol and Its Water-Saturated Solution: Molecular Dynamics and Free-Energy Perturbation Studies (1995) (129)
- A new water potential including polarization: Application to gas‐phase, liquid, and crystal properties of water (1990) (128)
- Molecular Dynamics Studies of the Properties of Water around Simple Organic Solutes (1996) (126)
- Theory of the Hydrogen Bond: Ab Initio Calculations on Hydrogen Fluoride Dimer and the Mixed Water–Hydrogen Fluoride Dimer (1970) (124)
- Nature of the hydrogen bond. Dimers involving electronegative atoms of the first row (1971) (123)
- A theoretical study of tautomerism in the gas phase and aqueous solution: a combined use of state-of-the-art ab initio quantum mechanics and free energy perturbation methods (1987) (122)
- Calculation of protein tertiary structure. (1976) (122)
- An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. (2001) (121)
- Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA. (1991) (121)
- Probing protein stability with unnatural amino acids. (1992) (119)
- Theory of the strong hydrogen bond. Ab initio calculations on HF2- and H5O2+1a (1970) (116)
- The lag between the Hamiltonian and the system configuration in free energy perturbation calculations (1989) (116)
- Computer modeling of the interactions of complex molecules (1990) (115)
- A molecular dynamics simulation of double-helical B-DNA including counterions and water. (1985) (113)
- Calculation of the free energy of association of nucleic acid bases in vacuo and water solution (1988) (112)
- Free energy perturbation simulations of the inhibition of thermolysin: prediction of the free energy of binding of a new inhibitor (1989) (112)
- The overlooked bond‐stretching contribution in free energy perturbation calculations (1991) (110)
- Molecular mechanics simulation of protein-ligand interactions: binding of thyroid hormone analogs to prealbumin (1982) (110)
- Hydrogen bonded dimers and polymers involving hydrogen fluoride, water, and ammonia (1970) (108)
- A molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix–coil transitions (1991) (107)
- What determines the strength of noncovalent association of ligands to proteins in aqueous solution? (1993) (106)
- A new method for carrying out free energy perturbation calculations: Dynamically modified windows (1989) (104)
- Automatic parameterization of force field by systematic search and genetic algorithms (2001) (104)
- Protein model structure evaluation using the solvation free energy of folding. (1990) (104)
- Free energy calculations on protein stability: Thr-157 .fwdarw. Val-157 mutation of T4 lysozyme (1989) (104)
- Theoretical studies of basicity. Proton affinities, lithium(1+) ion affinities, and hydrogen-bond affinities of some simple bases (1977) (103)
- Molecular mechanics and dynamics studies of crown ether - cation interactions: free energy calculations on the cation selectivity of dibenzo-18-crown-6 and dibenzo-30-crown-10 (1989) (103)
- Simulation of formamide hydrolysis by hydroxide ion in the gas phase and in aqueous solution (1985) (101)
- A Ligand That Is Predicted to Bind Better to Avidin than Biotin: Insights from Computational Fluorine Scanning (2000) (101)
- Free energy of association of the 18-crown-6:K+ complex in water: a molecular dynamics simulation (1990) (99)
- Electrostatic potentials of proteins. 1. Carboxypeptidase A. (1976) (99)
- Solvation Model Based on Weighted Solvent Accessible Surface Area (2001) (96)
- Studies of nucleotide conformations and interactions. The relative stabilities of double‐helical B‐DNA sequence isomers (1981) (95)
- Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III). (1997) (95)
- Simulation of the solvation free energies for methane, ethane, and propane and corresponding amino acid dipeptides : a critical test of the bond-PMF correction, a new set of hydrocarbon parameters, and the gas phase-water hydrophobicity scale (1992) (94)
- Free Energy of Association of the K+:18-Crown-6 Complex in Water: A New Molecular Dynamics Study (1995) (92)
- Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. (2003) (92)
- Nature of steroid-glucocorticoid receptor interactions: thermodynamic analysis of the binding reaction. (1978) (91)
- A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. (1997) (91)
- Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes (1997) (90)
- Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions. (1985) (86)
- On the use of electrostatic potential derived charges in molecular mechanics force fields. The relative solvation free energy of cis‐ and trans‐N‐methyl‐acetamide (1991) (85)
- Calculation and prediction of binding free energies for the matrix metalloproteinases. (2000) (85)
- Molecular dynamics simulation studies of liquid acetonitrile: New six‐site model (2000) (84)
- Catalytic pathway of serine proteases: classical and quantum mechanical calculations (1991) (83)
- Application of distance geometry to protein tertiary structure calculations (1979) (83)
- A theoretical study of intramolecular hydrogen bonding in ortho-substituted phenols and thiophenols (1976) (82)
- A theoretical examination of solvatochromism and solute-solvent structuring in simple alkyl carbonyl compounds. Simulations using statistical mechanical free energy perturbation methods (1990) (82)
- Ranking ligand binding affinities with avidin: a molecular dynamics‐based interaction energy study (1999) (81)
- Molecular mechanics studies of enzyme-substrate interactions: the interaction of L- and D-N-acetyltryptophanamide with α-chymotrypsin (1983) (79)
- Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation (1993) (78)
- Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory (1995) (78)
- Combined ab initio and Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution (1998) (76)
- Molecular dynamics simulations of small peptides: Dependence on dielectric model and pH (1991) (76)
- Advancing beyond the atom‐centered model in additive and nonadditive molecular mechanics (1997) (76)
- Molecular dynamics studies of a DNA‐binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor (1992) (75)
- Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose (1998) (75)
- An SCF partitioning scheme for the hydrogen bond (1970) (75)
- Computational studies of the interaction of myoglobin and xenon. (1986) (74)
- Can the Lennard–Jones 6‐12 function replace the 10‐12 form in molecular mechanics calculations? (1991) (73)
- The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the x‐ray structure “maintained”? (1996) (73)
- Theoretical calculations of the hydrolysis energies of some "high-energy" molecules. 2. A survey of some biologically important hydrolytic reactions (1978) (72)
- PROTON AFFINITIES AND PHOTOELECTRON SPECTRA OF THREE-MEMBERED-RING HETEROCYCLES (1980) (70)
- Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution. (2001) (70)
- Quantum mechanical and molecular mechanical studies on a model for the dihydroxyacetone phosphate-glyceraldehyde phosphate isomerization catalyzed by triose phosphate isomerase (TIM) (1984) (70)
- Calculation of free energy changes in ion–water clusters using nonadditive potentials and the Monte Carlo method (1987) (69)
- Theoretical studies of drug-dinucleotide interactions. Empirical energy function calculations on the interaction of ethidium, 9-aminoacridine, and proflavin cations with the base-paired dinucleotides GpC and CpG (1979) (68)
- QM−FE and Molecular Dynamics Calculations on Catechol O-Methyltransferase: Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction (2000) (67)
- Determination of the relative binding free energies of peptide inhibitors to the HIV-1 protease. (1991) (67)
- Theoretical calculations on proton-transfer energetics: studies of methanol, imidazole, formic acid, and methaneethiol as models for the serine and cysteine proteases (1981) (66)
- Solvation Free Energies of Amides and Amines: Disagreement between Free Energy Calculations and Experiment (1995) (65)
- Theoretical investigations of the rotational barrier in anisole: an ab initio and molecular dynamics study (1990) (65)
- Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex. (1988) (65)
- Protein structure prediction with a combined solvation free energy-molecular mechanics force field (1993) (64)
- Noncovalent interactions (2008) (64)
- Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings. (1982) (63)
- Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. (2005) (63)
- Theoretical Study of Base-Catalyzed Amide Hydrolysis: Gas- and Aqueous-Phase Hydrolysis of Formamide (1999) (62)
- Many-body potential for molecular interactions (1988) (62)
- COMBINED LOCALLY ENHANCED SAMPLING AND PARTICLE MESH EWALD AS A STRATEGY TO LOCATE THE EXPERIMENTAL STRUCTURE OF A NONHELICAL NUCLEIC ACID (1998) (61)
- Use of restrained molecular dynamics in water to determine three‐dimensional protein structure: Prediction of the three‐dimensional structure of Ecballium elaterium trypsin inhibitor II (1989) (61)
- Molecular Dynamics Potential of Mean Force Calculations: A Study of the Toluene−Ammonium π-Cation Interactions (1996) (61)
- The effect of water models on the interaction of the sodium–chloride ion pair in water: Molecular dynamics simulations (1990) (60)
- Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides (2000) (60)
- Electrostatic potentials of proteins. 2. Role of electrostatics in a possible catalytic mechanism for carboxypeptidase A. (1976) (60)
- Crown ether-neutral molecule interactions studied by molecular mechanics, normal mode analysis, and free energy perturbation calculations. Near quantitative agreement between theory and experimental binding free energies (1989) (60)
- Investigating the binding specificity of U1A-RNA by computational mutagenesis. (2000) (59)
- Molecular dynamics studies of calixspherand complexes with alkali metal cations: calculation of the absolute and relative free energies of binding of cations to a calixspherand (1992) (59)
- A simulation of the sulfur attack in catalytic pathway of papain using molecular mechanics and semiempirical quantum mechanics (1990) (58)
- Molecular mechanical studies of inclusion of alkali cations into anisole spherands (1985) (58)
- Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. (1997) (57)
- A new technique to calculate low-energy conformations of cyclic molecules utilizing the ellipsoid algorithm and molecular dynamics: application to 18-crown-6 (1988) (57)
- Hydrophobic solvation of methane and nonbond parameters of the TIP3P water model (1995) (56)
- Molecular Dynamics Simulations Find That 3‘ Phosphoramidate Modified DNA Duplexes Undergo a B to A Transition and Normal DNA Duplexes an A to B Transition (1997) (56)
- Computational protein folding: From lattice to all-atom (2001) (56)
- Molecular‐mechanics studies on d(CGCGAATTCGCG)2 and dA12·dT12: An illustration of the coupling between sugar repuckering and DNA twisting (1982) (55)
- Closing of the Nucleotide Pocket of Kinesin-Family Motors upon Binding to Microtubules (2003) (55)
- Quantum and molecular mechanical studies on alanyl dipeptide (1984) (54)
- Theory of hydrogen bond directionality (1972) (54)
- Molecular dynamics simulations study of the free energy of association of 9-methyladenine and 1-methylthymine bases in water (1990) (54)
- Metabolism of sirolimus and its derivative everolimus by cytochrome P450 3A4: insights from docking, molecular dynamics, and quantum chemical calculations. (2001) (54)
- The structure of d(CGCGAAT[]TCGCG) . d(CGCGAATTCGCG); the incorporation of a thymine photodimer into a B-DNA helix. (1984) (53)
- Thyroxine analogues. 23. Quantitative structure-activity correlation studies of in vivo and in vitro thyromimetic activities. (1977) (52)
- 2.1 and 1.8 Å Average Cα RMSD Structure Predictions on Two Small Proteins, HP-36 and S15 (2001) (52)
- Unrestrained Molecular Dynamics of Photodamaged DNA in Aqueous Solution (1997) (52)
- Ab initio SCF and MP2 calculations on four low-energy conformers of N-acetyl-N'-methylalaninamide (1992) (52)
- A method of describing the charge distribution in simple molecules (1978) (52)
- Derivation of fluorine and hydrogen atom parameters using liquid simulations (1992) (51)
- Electronic structure of Li–H2O and related neutral molecular complexes, including Al–H2O (1978) (50)
- A distance geometry study of ring systems (1983) (50)
- Inclusion of solvation free energy with molecular mechanics energy: Alanyl dipeptide as a test case (1992) (50)
- Monte Carlo simulation of aqueous solutions of Li+ and Na+ using many‐body potentials. Coordination numbers, ion solvation enthalpies, and the relative free energy of solvation (1990) (49)
- Molecular‐mechanical studies of Z‐DNA: A comparison of the structural and energetic properties of Z‐ and B‐DNA (1982) (49)
- Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations (2004) (49)
- Hydration number of lithium(1+) ion (1974) (49)
- Solvation Free Energies of the Nucleic Acid Bases (1996) (48)
- Conformational sampling and ensemble generation by molecular dynamics simulations: 18‐Crown‐6 as a test case (1992) (48)
- Monte Carlo simulation studies of the solvation of ions. 2. Glycine zwitterion (1988) (48)
- DO ENZYMES STABILIZE TRANSITION STATES BY ELECTROSTATIC INTERACTIONS OR PKA BALANCE : THE CASE OF TRIOSE PHOSPHATE ISOMERASE (TIM) ? (1995) (48)
- A water dimer potential based on ab initio calculations using Morokuma component analyses (1985) (48)
- The electronic structure of the HCN dimer and trimer (1972) (47)
- The nature of enzyme catalysis in trypsin. (1986) (47)
- Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations. (1999) (47)
- Free energy calculation on base specificity of drug – DNA interactions: Application to daunomycin and acridine intercalation into DNA (1990) (46)
- Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide. (2000) (46)
- Molecular mechanical simulations on double intercalation of 9-amino acridine into d(CGCGCGC) X d(GCGCGCG): analysis of the physical basis for the neighbor-exclusion principle. (1987) (46)
- Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions (1996) (46)
- Prediction of homologous protein structures based on conformational searches and energetics (1990) (46)
- Monte Carlo simulation studies of the solvation of ions. 1. Acetate anion and methylammonium cation (1986) (45)
- Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures (1999) (45)
- Comparison of ab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems (1992) (45)
- Molecular mechanical calculations on the interaction of ethidium cation with double‐helical DNA (1985) (42)
- Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. (2001) (42)
- Quantitative relationships between steroid structure and binding to putative progesterone receptors. (1977) (42)
- Theoretical prediction of the existence and properties of the lithium hydride dimer (1972) (41)
- A Simulation of the Catalytic Mechanism of Aspartylglucosaminidase Using ab Initio Quantum Mechanics and Molecular Dynamics (1997) (41)
- Theory of macromolecule-ligand interactions (1994) (41)
- Inhibition of carbonic anhydrase (1991) (41)
- Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces. (2004) (41)
- A comparison of the AM1 and PM3 semiempirical models for evaluating model compounds relevant to catalysis by serine proteases (1991) (40)
- Molecular dynamics studies of U1A-RNA complexes. (1999) (40)
- Molecular dynamics free energy simulations: Influence of the truncation of long‐range nonbonded electrostatic interactions on free energy calculations of polar molecules (1994) (40)
- A molecular orbital study of the benzene oxide-oxepin valence isomerization (1980) (40)
- A theory of anomalous water. (1970) (40)
- Theory of complex molecular interactions: computer graphics, distance geometry, molecular mechanics, and quantum mechanics (1985) (40)
- Anchoring of ammonium cations to an 18-crown-6 binding site: molecular mechanics and dynamics study (1989) (40)
- A novel class of molecular complexes: lithium-ammonia, lithium-water, lithium-hydrofluoric acid, lithium-hydrogen sulfide, sodium-water, and sodium-hydrofluoric acid (1977) (39)
- OH- versus SH- nucleophilic attack on amides: dramatically different gas-phase and solvation energetics (1988) (39)
- Computer modeling of actinomycin D interactions with double-helical DNA. (1986) (38)
- Bifurcated vs. linear hydrogen bonds: dimethyl phosphate and formate anion interactions with water (1983) (38)
- Amide-water hydrogen bonding (1972) (38)
- HCl and HF proton donors: a theoretical study (1974) (37)
- Investigating the Anomalous Solvation Free Energies of Amines with a Polarizable Potential (1996) (37)
- Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics (1997) (36)
- Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1 (2000) (36)
- Conformational preferences of substituted prolines in the collagen triple helix. (2002) (36)
- The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors (1998) (36)
- Computed free energy differences between point mutations in a collagen-like peptide. (2001) (36)
- The structure of the H3O+ (hydronium) ion (1973) (36)
- Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd. (2001) (35)
- Calculation of Ionization Potentials and C−H Bond Dissociation Energies of Toluene Derivatives (1996) (35)
- Molecular‐Mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG)·d(CGCGAATTCGCG) (1984) (35)
- Simple model for the effect of Glu165----Asp165 mutation on the rate of catalysis in triose phosphate isomerase. (1986) (35)
- Ab initio calculations on the structure and nature of the hydrogen bonded complex H2S ⋅⋅⋅ HF (1984) (35)
- Molecular dynamics characterization of the active cavity of carboxypeptidase A and some of its inhibitor adducts (1992) (35)
- A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP. (2002) (35)
- Dimers of lithium fluoride and sodium hydride (1973) (34)
- Molecular dynamics simulations of "loop closing" in the enzyme triose phosphate isomerase. (1987) (34)
- AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed‐memory hypercube computers (1993) (34)
- Free energy calculations on the relative solvation free energies of benzene, anisole and 1,2,3-trimethoxybenzene : theoretical and experimental analysis of aromatic methoxy solvation (1991) (34)
- CALCULATING THE ABSOLUTE FREE ENERGY OF ASSOCIATION OF NETROPSIN AND DNA (1999) (34)
- Stabilizing and destabilizing effects of placing beta-branched amino acids in protein alpha-helices. (1994) (34)
- Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis? (2002) (33)
- An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase. (2001) (33)
- On the role of uniform and mixed sugar puckers in DNA double-helical structures (1985) (33)
- The calculated free energy effects of 5‐methyl cytosine on the B to Z transition in DNA (1990) (32)
- Molecular mechanical studies of proflavine and acridine orange intercalation. (1981) (32)
- Why Does Trypsin Cleave BPTI so Slowly (2000) (32)
- A molecular mechanical study of netropsin‐DNA interactions (1986) (31)
- Calculation of Chloroform/Water Partition Coefficients for the N-Methylated Nucleic Acid Bases (1997) (31)
- Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches. (1990) (31)
- Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction. (2001) (30)
- Quantitation of long-range effects in steroids by molecular orbital calculations. (1973) (30)
- Theoretical investigations of novel nucleic acid bases (1992) (30)
- Photoelectron spectra of psychotropic drugs. 6. Relationships between the physical properties and pharmacological actions of amphetamine analogues. (1981) (30)
- Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method (1999) (30)
- The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin. (2006) (30)
- How transferable are hydrogen parameters in molecular mechanics calculations? (1992) (29)
- Hydration of ammonium fluoride (1976) (29)
- Conformations of the noncovalent and covalent complexes between mitomycins A and C and d(GCGCGCGCGC)2 (1986) (28)
- A conformational analysis of phosphoric acid, dihydrogen phosphate(1-), hydrogen phosphate(2-), and related model compounds (1977) (28)
- Finding potential DNA-binding compounds by using molecular shape (1994) (28)
- Molecular Dynamics Simulation of Nucleic Acids (2001) (28)
- Chemical shifts in paramagnetic gas mixtures (1972) (28)
- Molecular mechanical studies of base‐pair opening in d(CGCGC):d(GCGCG), dG5·dC5, d(TATAT):d(ATATA), and dA5·dT5 in the B and Z forms of DNA (1984) (28)
- A molecular mechanical model that reproduces the relative energies for chair and twist‐boat conformations of 1,3‐dioxanes (1995) (27)
- Evaluating the assumptions underlying force field development and application using free energy conformational maps for nucleosides (1991) (26)
- Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC).d(GCCAACTTGCG): comparison of simulation results with experiment. (1994) (26)
- Molecular Dynamics Free Energy Perturbation Calculations: Influence of Nonbonded Parameters on the Free Energy of Hydration of Charged and Neutral Species (1994) (26)
- Determination of solvation free energy using molecular dynamics with solute Cartesian mapping: An application to the solvation of 18‐crown‐6 (1992) (26)
- Simulations of the B‐DNA molecular dynamics of d(CGCGAATTCGCG)2 and d(GCGCGCGCGC)2: An analysis of the role of initial geometry and a comparison of united and all‐atom models (1990) (26)
- Trimethylamine-SO2, the prototype strong charge-transfer complex (1978) (26)
- Methylenimmonium ion and the role of resonance and inductive stabilization in carbonium ions (1973) (26)
- Computational and Experimental Studies of (2,2)-Bis(indol-1-yl-methyl)acetate Suggest the Importance of the Hydrophobic Effect in Aromatic Stacking Interactions (1999) (26)
- Molecular mechanical studies of d(CGTACG)2: complex of triostin A with the middle A - T base pairs in either Hoogsteen or Watson-Crick pairing. (1986) (26)
- Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989)). (1991) (25)
- Alkali Cation Extraction by 18-Crown-6 and Its Derivatives: A Free Energy Perturbation Study (1998) (25)
- An analysis of the sequence dependence of the structure and energy of A‐ and B‐DNA models using molecular mechannics (1983) (25)
- Computerized selection of potential DNA binding compounds. (1990) (25)
- Peptide mimetics as enzyme inhibitors: Use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor (1993) (25)
- ACCURATE SOLVATION FREE ENERGIES OF ACETATE AND METHYLAMMONIUM IONS CALCULATED WITH A POLARIZABLE WATER MODEL (1994) (25)
- A model equation for the analysis of noncovalent intermolecular interactions (1980) (24)
- Hydrogen Bonding and Donor—Acceptor Interactions (1977) (24)
- 1. Mapping Long-Range Interactions in -Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations (2005) (24)
- Designing an Optimum Guest for a Host Using Multimolecule Free Energy Calculations: Predicting the Best Ligand for Rebek's “Tennis Ball” (1998) (24)
- QUANTITATION AND NATURE OF THE MACROCYCLIC EFFECT : K+ COMPLEXATION WITH 18-CROWN-6 AND PENTAGLYME (1995) (24)
- Substituent effects on proton affinities of simple molecules (1974) (24)
- LIGAND BINDING IN THE CATALYTIC ANTIBODY 17E8. A FREE ENERGY PERTURBATION CALCULATION STUDY (1997) (24)
- Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48 G 7 (1999) (23)
- A negative electrostatic determinant mediates the association between the Escherichia coli trp repressor and its operator DNA (1994) (23)
- pKa, MM, and QM studies of mechanisms of β‐lactamases and penicillin‐binding proteins: Acylation step (2002) (23)
- Theoretical and experimental studies of biotin analogues that bind almost as tightly to streptavidin as biotin. (2002) (23)
- Molecular dynamics and free energy calculations on the peculiar bimodal alkali ion selectivity of an 8-subunit cavitand (1994) (23)
- Why do A.T base pairs inhibit Z-DNA formation? (1990) (23)
- Computer simulation studies of spherands, crowns and porphyrins: application of computer graphics, distance geometry, molecular mechanics and molecular dynamics approaches (1989) (23)
- THE EFFECTS OF BASIS SET AND BLOCKING GROUPS ON THE CONFORMATIONAL ENERGIES OF GLYCYL AND ALANYL DIPEPTIDES. A HARTREE-FOCK AND MP2 STUDY (1997) (23)
- Monte Carlo simulations of the solvation of the dimethyl phosphate anion (1985) (23)
- Molecular dynamics simulation studies of liquid acetonitrile: New six-site model (2000) (22)
- Application of molecular dynamics and free energy perturbation methods to metalloporphyrin‐ligand systems ii: Co and dioxygen binding to myoglobin (1993) (22)
- Free energy calculations of the mutation of Ile96-->Ala in barnase: contributions to the difference in stability. (1996) (22)
- Free energy perturbation calculations on binding and catalysis after mutating threonine 220 in subtilisin. (1991) (22)
- Chelate effect in cyclodextrin dimers: a computational (MD, MM/PBSA, and MM/GBSA) study. (2006) (22)
- Intramolecular nonbonded attractions in molecules (1974) (22)
- An NMR study of the interaction of daunomycin with dinucleotides and dinucleoside phosphates. (1980) (22)
- Amino substituent effect on the properties of ionic compounds (1975) (21)
- Molecular dynamics simulations suggest that the Eco RI kink is an example of molecular strain. (1994) (21)
- Macrocyclic receptor chemistry: Experimental and theoretical studies on molecular recognition (1983) (21)
- Can one predict protein stability? An attempt to do so for residue 133 of T4 lysozyme using a combination of free energy derivatives, PROFEC, and free energy perturbation methods (1998) (21)
- QM-FE Calculations of Aliphatic Hydrogen Abstraction in Citrate Synthase and in Solution: Reproduction of the Effect of Enzyme Catalysis and Demonstration that an Enolate Rather than an Enol Is Formed (2000) (21)
- Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants. (1997) (21)
- THEORETICAL STUDIES OF HYDROGEN-BONDED DIMERS, COMPLEXES INVOLVING HF, H2O, NH3, HCL, H2S, PH3, HCN, HNC, HCP, CH2NH, H2CS, H2CO, CH4, CF3H, C2H2, C2H4, C6H6, F(-), AND H3O(+) (1975) (21)
- Molecular mechanics simulations on covalent complexes between polycyclic carcinogens and B-DNA. (1989) (21)
- Comparison of solution structures of mutant bovine pancreatic trypsin inhibitor proteins using two‐dimensional nuclear magnetic resonance (1992) (20)
- Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems. I. Carbon monoxide and dioxygen binding to four heme systems (1989) (20)
- Molecular mechanics simulations on covalent complexes between anthramycin and B DNA. (1986) (20)
- Theoretical Studies Suggest a New Antifolate as a More Potent Inhibitor of Thymidylate Synthase (2000) (20)
- Conformations of the 8-methylated and unmethylated ribohexamer r(CGCGCG)2 (1986) (20)
- Hydrogen bonding and the structure of the HFHCN dimer (1972) (20)
- Computational analysis of structural and energetic consequences of DNA methylation. (1989) (20)
- A theoretical study of intramolecular Diels-Alder and 1,3-dipolar cycloaddition stereoselectivity using ab initio methods, semiempirical methods, and a tandem quantum mechanic-molecular mechanic method (1992) (20)
- Calculations of the relative free energies of aqueous solvation of several fluorocarbons: A test of the bond potential of mean force correction (1993) (19)
- Free energy perturbation calculations involving potential function changes (1992) (19)
- The attractive rotational barrier in nitrosomethane (1970) (19)
- The structure of the water dimer (1971) (19)
- Free energy calculations on binding and catalysis by α‐lytic protease: The role of substrate size in the P1 pocket (1991) (19)
- Electrostatic potentials of deoxydinucleoside monophosphates. 1. Deoxydinucleoside monophosphates and actinomycin chromophore interactions. (1979) (18)
- A combined 2D-NMR and molecular dynamics analysis of the structure of the actinomycin D: d(ATGCAT)2 complex. (1989) (18)
- Molecular orbital studies of thyroid hormone analogs. (1973) (18)
- Walking on the free energy hypersurface of the 18‐crown‐6 ion system using free energy derivatives (1994) (18)
- Free energy component analysis: a study of the glutamic acid 165 .fwdarw. aspartic acid 165 mutation in triosephosphate isomerase (1989) (18)
- Observation of an A-DNA to B-DNA transition in a nonhelical nucleic acid hairpin molecule using molecular dynamics. (1997) (18)
- Quantum Mechanical Study of β-Lactam Reactivity: The Effect of Solvation on Barriers of Reaction and Stability of Transition States and Reaction Intermediates (1999) (18)
- Steric and electronic effects on carbon-13 nuclear magnetic resonance alpha, beta and gamma shifts and fluorine-19-carbon-13 coupling constants in 9 alpha-substituted cortisol derivatives. (1974) (18)
- Effects of nucleotide bromination on the stabilities of Z‐RNA and Z‐DNA: A molecular mechanics/thermodynamic perturbation study (1989) (18)
- CONFORMATIONS OF DEOXYDODECANUCLEOTIDES WITH PYRIMIDINE (6‐4) PYRIMIDONE PHOTOADDUCTS (1985) (18)
- INSIGHT INTO THE SPECIFICITY OF THYMIDYLATE SYNTHASE FROM MOLECULAR DYNAMICS AND FREE ENERGY PERTURBATION CALCULATIONS (1995) (17)
- Molecular Dynamics Simulations on Nucleic Acid Systems Using the Cornell et al. Force Field and Particle Mesh Ewald Electrostatics (1998) (17)
- A model for thyroid hormone--receptor interactions. (1979) (17)
- Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations (1999) (17)
- Molecular mechanics and dynamics calculations on (dA)10.(dT)10 incorporating distance constraints derived from NMR relaxation measurements. (1987) (17)
- Conformations of complexes between mitomycins and decanucleotides. 3. Sequence specificity, binding at C-10, and mitomycin analogues. (1988) (17)
- Molecular recognition by beta-cyclodextrin derivatives: FEP vs MM/PBSA study. (2001) (16)
- Applying Molecular and Materials Modeling (2010) (16)
- Ab initio self-consistent field calculations on molecular iodine-ammonia and hydrogen iodide-ammonia. The classic "charge-transfer" interaction, an example of gas-phase proton transfer, and the duality of Lewis acid sites on hydrogen iodide (1982) (16)
- Cyclic systems containing divalent hydroen symmetrically placed between sp2 hybridized electron-rich atoms. A new form of chemical bong? (1970) (16)
- State of the art in studying protein folding and protein structure prediction using molecular dynamics methods. (2001) (16)
- Ab initio calculations on aquated chloride (Cl-(H2O)14) clusters: comparison with the results from molecular dynamics simulations (1992) (16)
- Use of molecular dynamics and free energy perturbation calculations in anti-human immunodeficiency virus drug design. (1994) (15)
- Studies of the Mechanism of Glucocorticoid Hormone Action (1983) (15)
- Molecular recognition by β-cyclodextrin derivatives: molecular dynamics, free-energy perturbation and molecular mechanics/ Poisson–Boltzmann surface area goals and problems (2002) (15)
- Molecular dynamics studies of a DNA‐binding protein: 1. A comparison of the trp repressor and trp aporepressor aqueous simulations (1992) (15)
- A study of the biologically active conformers for prodine opiates and their derivatives (1984) (14)
- Understanding the thermodynamic stability of an RNA hairpin and its mutant. (1996) (14)
- Relative binding free energy calculations of inhibitors to two mutants (Glu46----Ala/Gln) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches. (1991) (14)
- Molecular Dynamics Simulations of DNA Double Helices: Studies of Sequence Dependence and the Role of Mismatch Pairs in the DNA Helix (1986) (14)
- Understanding substrate specificity in human and parasite phosphoribosyltransferases through calculation and experiment. (1999) (14)
- An Approach to the Application of Free Energy Perturbation Methods Using Molecular Dynamics: Applications to the Transformations of CH3OH → CH3CH3, H3O+ → NH+ 4, Glycine → Alanine, and Alanine → Phenylalanine in Aqueous Solution and t (1987) (14)
- The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach (2003) (14)
- Applications of Molecular and Materials Modeling (2002) (13)
- The structure and relative energies of C2H2X+ isomers (X = fluoro, hydroxyl, amino, chloro, and mercapto) (1978) (13)
- Molecular dynamics simulations of active site mutants of triosephosphate isomerase. (1990) (13)
- An ab initio molecular orbital study of the first step of the catalytic mechanism of thymidylate synthase: the Michael addition of sulfur and oxygen nucleophiles (1995) (13)
- Theoretical studies of the K+ affinities of bases: a comparison of K+ and Li+ affinities (1978) (13)
- The long range intermolecular potential of H2-H2 (1972) (13)
- The effect of methylation of the 6 oxygen of guanine on the structure and stability of double helical DNA. (1985) (13)
- Time evolution of NMR proton chemical shifts of an RNA hairpin during a molecular dynamics simulation (1996) (12)
- Theory of enzyme mechanisms (1992) (12)
- THEORETICAL STUDIES OF THE STRUCTURE AND ENERGIES OF BASE‐PAIRED NUCLEOTIDES AND THE DISSOCIATION KINETICS OF A PROFLAVINE‐DINUCLEOTIDE COMPLEX * (1981) (12)
- Conformations of complexes between mitomycin and decanucleotides. 2. Application of the model to mitomycin C derivatives. Extension to covalent binding with adenine. (1986) (12)
- Modeling Complex Molecular Interactions Involving Proteins and DNA a (1986) (12)
- two-dimensional nuclear magnetic resonance (1992) (11)
- Theoretical calculations on the geometric destabilization of 3′,5′- and 2′,3′-cyclic nucleotides (1980) (11)
- A diffusion–collision–adhesion model for the kinetics of myoglobin refolding (1980) (11)
- Calculation of the Φ-Ψ maps for alanyl and glycyl dipeptides with different additive and non-additive molecular mechanical models (1997) (11)
- 2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. (2001) (11)
- Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9 (2003) (11)
- A quantum chemical study of the type IV nucleophilic substitution reaction and dissociation of the .beta.-nicotinamide glycosyl bond in the gas phase using semiempirical PM3 calculations (1992) (11)
- The free energies for mutating S27 and W79 to alanine in streptavidin and its biotin complex: The relative size of polar and nonpolar free energies on biotin binding (1999) (11)
- An iterative approach to placing counterions around DNA. (1984) (11)
- Molecular dynamics study of the stability of staphylococcal nuclease mutants: component analysis of the free energy difference of denaturation. (1993) (11)
- Elucidating the Origin of Conformational Energy Differences in Substituted 1,3-Dioxanes: A Combined Theoretical and Experimental Study. (1996) (11)
- A conformational analysis of daunomycin considering D-ring repucker. (1982) (11)
- Molecular Dynamics and Free Energy Perturbation Study of Spherand Complexation with Metal Ions Employing Additive and Nonadditive Force Fields (1995) (11)
- Conformations of duplex structures formed by oligodeoxynucleotides covalently linked to the intercalator 2-methoxy-6-chloro-9-aminoacridine. (1987) (10)
- Structural changes by sulfoxidation of phenothiazine drugs (1992) (10)
- Gradient SHAKE: An improved method for constrained energy minimization in macromolecular simulations (1995) (10)
- QUANTITATIVE RELATIONS BETWEEN STEROID STRUCTURE AND BINDING TO PUTATIVE PROGESTERONE RECEPTORS (1977) (10)
- A molecular mechanical study of complexes formed between 4-nitroquinoline-N-oxide and dinucleoside phosphates. (1981) (9)
- Hydrogen‐bonding preferences in 2,6‐diaminopurine: uracil (thymine) and 8‐methyl adenine:uracil (thymine) complexes (1986) (9)
- Theoretical calculations of the hydrolysis energies of some high energy molecules. I. Phosphoric and carboxylic acid anhydrides (1975) (9)
- Molecular dynamics simulations of a highly charged peptide from an SH3 domain: Possible sequence–function relationship (2001) (9)
- Structure Predictions on Two Small Proteins , HP-36 and S 15 (9)
- An ab initio molecular orbital study of intramolecular H-bonding: 1,3 propanediol (1973) (9)
- The ammonia—sulfur trioxide interaction. An ab initio study (1978) (9)
- An analysis of the hard-soft Lewis acid-base concept and the Drago equation employing ab initio molecular orbital theory (1981) (9)
- Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations (2001) (9)
- Free Energy Perturbation Calculations of the Relative Binding Affinities of an 8-Subunit Cavitand for Alkali Ions in Methanol (1994) (8)
- Application of Free Energy Perturbation Calculations to the “Tennis Ball” Dimer: Why Is CF4 Not Encapsulated by This Host? (1996) (8)
- Analysis of the pharmacological properties of clozapine analogues using molecular electrostatic potential surfaces (1986) (8)
- Molecular‐mechanical studies of hormone–protein interactions: The interaction of T4 and T3 with prealbumin (1984) (8)
- Ab initio MO-SCF calculation on a model of anomalous water (1970) (8)
- QM and QM–FE simulations on reactions of relevance to enzyme catalysis: trypsin, catechol O-methyltransferase, β-lactamase and pseudouridine synthase (2000) (8)
- Molecular mechanical potential functions and their application to study molecular systems: Current Opinion in Structural Biology 1991, 1:201–212 (1991) (8)
- Binding of Organic Cations to a Cyclophane Host As Studied with Molecular Dynamics Simulations and Free Energy Calculations (1999) (8)
- Applications of free energy derivatives to analog design (1995) (8)
- Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement. (2002) (7)
- Molecular Modeling of Nucleic Acid Structure (2001) (7)
- Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup (1994) (7)
- Graphical visualization of mean hydration from molecular dynamics simulations. (1997) (7)
- Elucidating the Nature of Enzyme Catalysis Utilizing a New Twist on an Old Methodology: Quantum Mechanical—Free Energy Calculations on Chemical Reactions in Enzymes and in Aqueous Solution (2001) (7)
- Investigation of the Anomalous Solvation Free Energies of Amides and Amines: FEP Calculations in Cyclohexane and PS-GVB Calculations on Amide−Water Complexes (1998) (7)
- Molecular mechanics and dynamics in protein design. (1987) (7)
- Computational Study of the Structural, Energetical, and Acid-Base Properties of Calix(4)arenes. (1990) (7)
- Quantitative structure-activity relationships in the 2,4,5-ring substituted phenylisopropylamines. (1978) (7)
- Molecular Design of Fluorine-Containing Peptide Mimetics (1996) (7)
- A technique to study molecular recognition in drug design: Preliminary application of free energy derivatives to inhibition of a malarial cysteine protease (1996) (7)
- Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation (2001) (7)
- Free energy perturbation calculations on models of active sites: Applications to adenosine deaminase inhibitors (1990) (7)
- Molecular orbital calculations on suspected intermediates in oxidative amine metabolism. (1973) (7)
- Correlation of glucocorticoid and progestational activity with steric, electronic and hydrophobic parameters. (1975) (7)
- Chemical reaction mechanisms in vacuo, in solution and in enzyme fields: isomerization catalyzed by triose phosphate isomerase (TIM) (1996) (7)
- PHOTOELECTRON SPECTRA OF PSYCHOTROPIC DRUGS. 6. RELATIONSHIPS BETWEEN PHYSICAL PROPERTIES AND PHARMACOLOGICAL ACTIONS OF AMPHETAMINE ANALOGS (1982) (6)
- Theoretical Evidence Against the Existence of Polywater (1971) (6)
- Computer Simulation of Diffusion-Limited Chemical Reactions in Three Dimensions (1987) (6)
- A Comparison of the Energetics of Proton Transfer in the Serine and Cysteine “Charge Relay” Systems and the Role of the Protein Electrostatic Potential on the Proton Transfer Energetics (1979) (6)
- Chapter 2 Non-covalent forces of importance in biochemistry (1984) (6)
- CONFORMATIONAL ANALYSES OF PHOSPHOCREATINE AND N-METHYLCREATINE, A STERIC MODEL FOR PHOSPHOCREATINE (1976) (6)
- Free Energy Perturbation and Molecular Dynamics Studies of [16]Starand with Various Alkali Metal Ions (1999) (6)
- AMBER: A Program for Simulation of Biological and Organic Molecules (2002) (6)
- Application of the quantum mechanics and free energy perturbation methods to study molecular processes (1987) (6)
- The Role of the Electrostatic Potential in Modeling Hydrogen Bonding and Other Non-Covalent Interactions (1981) (6)
- Ab Initio Quantum Mechanical and Molecular Dynamical Study of Intra- and Intermolecular Anhydride Formation (1999) (6)
- STERIC AND ELECTRONIC EFFECTS ON CARBON-13 NUCLEAR MAGNETIC RESONANCE ALPHA,BETA, AND GAMMA SHIFTS AND FLUORINE-19-CARBON-13 COUPLING CONSTANTS IN 9ALPHA-SUBSTITUTED CORTISOL DERIVATIVES (1974) (6)
- Molecular Modeling of Nucleic Acid Structure: Setup and Analysis (2001) (6)
- Ab initio explorative survey of the mechanism catalyzed by mandelate racemase (1997) (5)
- Molecular Modeling of Nucleic Acid Structure: Energy and Sampling (2001) (5)
- The rotational barrier in dimethyl acetylene and related molecules (1974) (5)
- Free energy component analysis: application to the "Z-phobicity" of A-T base pairs. (1993) (5)
- Relative energies of diprotonation of small neutral molecules (1977) (5)
- MOLECULAR ORBITAL STUDIES OF THYROID HORMONE ANALOGS (1974) (5)
- Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics (1996) (5)
- Are There Water-Bridge-Induced Hydrophilic Interactions? (1996) (5)
- Energy component analysis calculations on neutral atom …︁ base interactions (1985) (5)
- The Nature of Molecular Recognition: Examples from Host/Guest Chemistry (1994) (5)
- Molecular mechanisms of glucocorticoid hormone action. (1982) (5)
- Monte Carlo Simulation Studies of the Solvation of Ions. Part 1. Acetate‐Anion and Methylammonium Cation (1986) (4)
- Application of free-energy decomposition to determine the relative stability of R and S oligodeoxyribonucleotide methylphosphonates. (1991) (4)
- Conformational Flexibility of Nucleic Acids (1983) (4)
- What can theory say about the existence and properties of anomalous water (1971) (4)
- Molecular mechanical studies on left‐ and right‐handed B‐DNA (1987) (3)
- OH- versus SH- Nucleophilic Attack on Amides: Dramatically Different Gas-Phase and Solvation Energetics. (1989) (3)
- MM-PBSA Applied to Computer-Assisted Ligand Design (2003) (3)
- Binding Free Energy and Extraction Selectivity Calculations of Anisole and Phenanthroline Spherands (1999) (3)
- Theoretical Simulations on d(CGCGAATTCGCG)2 with cis-syn Thymine–Thymine Cyclobutane Dimer (1993) (3)
- Barriers to rotation in acylguanidines and acylguanidinium ions (1981) (3)
- Energy component analysis calculations on interactions involving iodine and hydrogen iodide (1983) (3)
- Conformations of the Noncovalent and Covalent Complexes Between Mitomycins A and C and d(GCGCGCGCGC)2. (1986) (3)
- CONFORMATION OF THE PROGESTERONE SIDE CHAIN: RESOLUTION OF THE APPARENT CONFLICT BETWEEN X‐RAY DATA AND FORCE‐FIELD CALCULATIONS USING MM2 (1982) (3)
- Free Energy Calculations on the Relative Solvation Free Energies of Benzene, Anisole, and 1,2,3‐Trimethoxybenzene: Theoretical and Experimental Analysis of Aromatic Methoxy Solvation. (1991) (2)
- A comparison of theoretical models for anomalous water (1971) (2)
- Quantum Mechanical Calculations of Nucleophilic Attack in the Pseudouridine Synthesis Reaction (1999) (2)
- Inhibition of carbonic anhydrase. [Erratum to document cited in CA115(3):24912t] (1992) (2)
- Computational Approaches to the Study of Protein — Ligand Interactions (1987) (2)
- Recent Advances in Structure-Based Ligand Design Using Molecular Dynamics and Monte Carlo Methods (1998) (2)
- THE HYDRATION NUMBER OF LI( (1974) (2)
- Molecular mechanical calculations on a macrocyclic receptor: the 222 cryptand and its alkali complexes (1985) (2)
- Drug-Target Binding Forces: Advances in Force Field Approaches (2003) (2)
- Quantitation of chemical and biological effects in steroids by Hansch-type and molecular orbital calculations. (1976) (1)
- Molecular graphics of neuroleptics: New perspectives in neuro-psychopharmacology and drug design (1987) (1)
- Grand challenges in computational science: Simulations on biological macromolecules (1989) (1)
- Inductive versus polarization effects on ionization potentials (1983) (1)
- MOLE: a system for quantum chemistry. II. Recent developments (2009) (1)
- Theoretical studies of thyroid hormone analogs. (1976) (1)
- The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme. (1991) (1)
- Conformations of Complexes between Mitomycin and Decanucleotides. (1986) (1)
- THYROXINE ANALOGS. 23. QUANTITATIVE STRUCTURE-ACTIVITY CORRELATION STUDIES OF F IN VIVO AND IN VITRO THYROMIMETIC ACTIVITIES (1977) (1)
- New Free Energy Calculation Methods for Structure-Based Drug Design and Prediction of Protein Stability (1999) (1)
- A Theoretical Study of Tautomerism in the Gas Phase and Aqueous Solution: A Combined Use of “State-of-the-Art” ab initio Quantum Mechanics and Free Energy Perturbation Methods (1988) (1)
- Chiroptical properties and optical and molecular orbital calculations for dictyopterenes A and B (1979) (1)
- Molecular dynamics simulations can reproduce the subtle differences in NADP and NHDP binding to isocitrate dehydrogenase (1999) (1)
- Gordon Research Conference on Computational Chemistry Held in Plymouth, New Hampshire on 4-8 July 1988 (1988) (1)
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- Computer Simulation Methods as Applied to Site-Specific Mutations (1990) (1)
- Free Energy Calculations: Applications to Chemical and Biochemical Phenomena (1994) (1)
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- Molecular dynamics simulations on protein folding and protein structure prediction (2000) (0)
- MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED AND THE ELECTRON PARAMAGNETIC RESONANCE (EPR) SPIN PROBE SSL-NANDP BOUND AT THE NUCLEOTIDE SITE (2004) (0)
- A molecular dynamics simulation of double-helical B-DNA including counterions and water ( DNA hydration / DNA dynamics / DNA structure / DNA sugar pucker / electrostatic interactions ) (0)
- Molecular dynamics simulations of d ( CG-CGA ) d ( TCG-CG ) with and without " hydrated " counterions ( DNA / molecular mechanics / conformational analysis / electrostatic effects ) (0)
- Elucidating the roles of Ca plus plus and Mg plus plus in ATP hydrolysis in myosin from first principles and classical mechanical calculations (2001) (0)
- MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED AND WITH ADP BOUND AT THE NUCLEOTIDE SITE (2004) (0)
- Molecular Mechanical Studies on the B → Z Energetics of DNA Sequences (1988) (0)
- Additions and Corrections - Hydration of NH4F (1976) (0)
- Simulation of complex molecules—computational requirements for the 1980's (1985) (0)
- Electrostatic Properties of Proteins: Role of the Aqueous Solution in Determining Protein Secondary and Tertiary Structure (1976) (0)
- Investigation of the substrate binding and phosphate transfer in adenylate kinase by molecular mechanics. (1988) (0)
- Differentiation of D- and L-Thyroxine by the plasma protein prealbumin (2009) (0)
- The Use of Molecular Dynamics and Free Energy Perturbation Approaches in Simulating the Properties of Macromolecules and Their Binding to Ligands (1990) (0)
- No Job Name (0)
- Metal Cations in Biological Systems: Modeling Metal Ions in Ionophores and DNA (1997) (0)
- Challenges in Computer Modeling Complex Molecular Systems (1992) (0)
- KOLLMAN energy : Alanyl dipeptide as a test case Inclusion of solvation free energy with molecular mechanics (2006) (0)
- Theoretical Study of Base-Catalyzed Amide Hydrolysis: Gas- and Aqueous-Phase Hydrolysis of Formamide. (1999) (0)
- Electrostatic potential molecular surfaces ( nucleic acids / proteins / drug-nucleic acid interactions / protein-ligand interactions ) (2003) (0)
- Applications: Pharmaceuticals and Life Sciences (2002) (0)
- Car-Parrinello molecular dynamics applied to the ATP hydrolysis reaction in myosin (2001) (0)
- A MODEL FOR THYROID HORMONE-RECEPTOR INTERACTIONS (1979) (0)
- Conformation and electrostatic potential surfaces of opiates: Relationship to µ- and λ-site binding (1986) (0)
- ELECTROSTATIC FORCES BETWEEN LIGANDS AND MACROMOLECULES. (1984) (0)
- Conformations of the 8-Methylated and Unmethylated Ribohexamer r(CGCGCG)2. (1986) (0)
- CORRELATION OF GLUCOCORTICOID AND PROGESTATIONAL ACTIVITY WITH STERIC, ELECTRONIC AND HYDROPHOBIC PARAMETERS (1976) (0)
- Announcement (1987) (0)
- THE NH2 SUBSTITUENT EFFECT ON THE PROPERTIES OF IONIC COMPOUNDS (1975) (0)
- Challenges and new directions in computer assisted structure based drug design (1997) (0)
- Introduction: Theoretical chemistry in biology: From molecular structure to functional mechanisms (1998) (0)
- A NOVEL CLASS OF MOLECULAR COMPLEXES- LITHIUM-AMMONIA, LITHIUM-WATER, LITHIUM-HYDROFLUORIC ACID, LITHIUM-HYDROGEN SULFIDE, SODIUM-WATER, AND SODIUM-HYDROFLUORIC ACID (1977) (0)
- Perspective on “Molecular dynamics study of liquid water” (2000) (0)
- Picture chemistry! (1984) (0)
- Conformations of deoxydinucleoside phosphates containing pyrimidine-pyrimidine photodimers. (1990) (0)
- MOLECULAR ORBITAL CALCULATIONS ON SUSPECTED INTERMEDIATES IN OXIDATIVE AMINE METABOLISM (1973) (0)
- Hydrogen bonding (1999) (0)
- Determination of Solvation Free Energy Using Molecular Dynamics with Solute Cartesian Mapping: An Application to the Solvation of 18‐Crown‐ 6. (1993) (0)
- Molecular Mechanics and Dynamics Studies of Crown Ether-Cation Interactions: Free Energy Calculations on the Cation Selectivity of Dibenzo-18-crown-6 and Dibenzo-30-crown-10. (1989) (0)
- Applications of computer simulation approaches to proteins and nucleic acids (1990) (0)
- A molecular dynamics simulation of double-helical B-DNA (0)
- CLd2 COMPUTER SIMULATIONS ON ORGANIC MOLECULES (1988) (0)
- HYDRATATION VON KATIONEN (1973) (0)
- ELECTROSTATIC POTENTIALS OF DEOXYDINUCLEOSIDE MONOPHOSPHATES. 1. DEOXYDINUCLEOSIDE MONOPHOSPHATES AND ACTINOMYCIN CHROMOPHORE INTERACTIONS (1980) (0)
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